20.109(S13):Module 1

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==Module 1==
==Module 1==
   
   
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'''Instructors:''' [[User:Shannon K. Alford |Shannon Hughes-Alford]], [http://web.mit.edu/be/people/runstadler.shtml Jonathan Runstadler], and [[User:AgiStachowiak| Agi Stachowiak]]
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'''Instructors:''' [[User:Shannon K. Alford |Shannon Hughes]], [http://web.mit.edu/be/people/runstadler.shtml Jonathan Runstadler], and [[User:AgiStachowiak| Agi Stachowiak]]
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'''TA:'''  
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'''TA:''' [[User:Ian_Tay |Ian Tay]]
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<font color=red> S13 notes: Brand-new module! No precedent. Sometime before February it will all be laid out in writing. For now, I'll sketch out a few highlights.</font color>
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In this module, you'll complete two mini-investigations while gaining foundational skills -- in laboratory techniques, data analysis, and both written and oral communication -- that will serve you well in the remaining two modules. Throughout, host–pathogen interactions and their implications for human health will be a unifying theme. You'll study two pathogen types that can infect birds: bacteria and fungus. As a class, you will perform a phylogenetic analysis of the bacteria found in two distinct bird populations and look for differences. This study has parallels to recent investigations of human microbiome diversity that shed light on variations in metabolism, susceptibility to infection, etc. We will also learn what bacteria you might be exposed to the next time you accidentally encounter bird feces! As individuals, you will design and test primers for diagnosing infection with the fungus microsporidia. It has previously been found that microsporidia infections are common in several bird populations that have contact with humans -- aquatic birds that may visit reservoirs or beaches, pets such as parrots and lovebirds, and pests such as pigeons -- and it is speculated that zoonotic transfer may occur. Although most people can rapidly clear such an infection, immunocompromised people such as children, the elderly, and HIV-infected individuals are at risk for serious complications. Improving the sensitivity and/or specificity of microsporidia diagnosis could thus be useful in environmental testing and subsequent health care recommendations. Your class-wide study of animal/environmental bacteria populations has similar implications for managing disease risk.
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In this module, you'll complete two mini-investigations while gaining foundational skills -- in laboratory techniques, data analysis, and both written and oral communication -- that will serve you well in the remaining two modules. You'll study two different types of pathogens that can infect birds: bacteria and fungus. As a class, you will perform a phylogenetic analysis of the bacteria found in two distinct bird populations and look for trends. [Framing of broader purpose?] As individuals, you will design and test primers for diagnosing infection with the fungus microsporidia. It has been previously found that microsporidia infections are common in several bird populations that have contact with humans -- aquatic birds that may visit reservoirs or beaches, pets such as parrots and lovebirds, and pests such as pigeons -- and it is speculated that zoonotic transfer may occur. Although most people can rapidly clear such an infection, immunocompromised people such as children, the elderly, and HIV-infected individuals are at risk for serious complications. Improving the sensitivity and/or specificity of avian microsporidia diagnosis could thus be useful in environmental testing and health care.  
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We thank the Runstadler lab for access to bird samples (pre-screened for flu and everything!), and especially Wendy Puryear for helpful technical discussions as this module was developed. We also thank Professor Karen Snowden at Texas A & M University for access to microsporidia spores and for invaluable advice about imaging methods for identifying microsporidia.
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We thank the Runstadler lab for access to bird samples (pre-screened for flu and everything!), and especially Wendy Puryear for helpful technical discussions as this module was developed.
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[[Image:S13-M1 concept-overview.jpg|thumb|450px|center|'''Module 1 Conceptual Overview.''' Experimental goals are shown in yellow, related concepts in blue, and related application areas in green. Stars span both experiments, while triangles are associated with a single experiment.]]
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[[20.109(S13):X (Day1)| Module 1 Day 1: X]]<br>
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[[20.109(S13):Context-setting and primer design (Day1)| Module 1 Day 1: Context-setting and primer design]]<br>
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[[20.109(S13):X (Day2)| Module 1 Day 2: X]]<br>
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[[20.109(S13):DNA extraction (Day2)| Module 1 Day 2: DNA extraction]]<br>
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[[20.109(S13):X (Day3)| Module 1 Day 3: X]]<br>
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[[20.109(S13):PCR and paper discussion (Day3)| Module 1 Day 3: PCR and paper discussion]]<br>
Note: 1 week between day 3 and day 4.
Note: 1 week between day 3 and day 4.
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[[20.109(S13):X (Day4)| Module 1 Day 4: X]]<br>
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[[20.109(S13):DNA cloning (Day4)| Module 1 Day 4: DNA cloning]]<br>
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[[20.109(S13):X (Day5)| Module 1 Day 5: X]]<br>
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[[20.109(S13):DNA sequencing and primer analysis (Day5)| Module 1 Day 5: DNA sequencing and primer analysis]]<br>
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[[20.109(S13):Xv (Day6)| Module 1 Day 6: X]]<br>
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[[20.109(S13):Journal club I (Day6)| Module 1 Day 6: Journal club I]]<br>
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[[20.109(S13):X (Day7)| Module 1 Day 7: X]]<br>
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[[20.109(S13):Phylogenetic analysis (Day7)| Module 1 Day 7: Phylogenetic analysis]]<br>
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[[20.109(S13):Journal club (Day8)| Module 1 Day 8: Journal club]]<br>
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[[20.109(S13):Journal club II (Day8)| Module 1 Day 8: Journal club II]]<br>
[[20.109(S13): DNA engineering report | Laboratory Report]]<br>
[[20.109(S13): DNA engineering report | Laboratory Report]]<br>

Current revision

20.109(S13): Laboratory Fundamentals of Biological Engineering

Home        Schedule Spring 2013        Assignments       
DNA Engineering        Protein Engineering        Cell Engineering              

Module 1

Instructors: Shannon Hughes, Jonathan Runstadler, and Agi Stachowiak

TA: Ian Tay

In this module, you'll complete two mini-investigations while gaining foundational skills -- in laboratory techniques, data analysis, and both written and oral communication -- that will serve you well in the remaining two modules. Throughout, host–pathogen interactions and their implications for human health will be a unifying theme. You'll study two pathogen types that can infect birds: bacteria and fungus. As a class, you will perform a phylogenetic analysis of the bacteria found in two distinct bird populations and look for differences. This study has parallels to recent investigations of human microbiome diversity that shed light on variations in metabolism, susceptibility to infection, etc. We will also learn what bacteria you might be exposed to the next time you accidentally encounter bird feces! As individuals, you will design and test primers for diagnosing infection with the fungus microsporidia. It has previously been found that microsporidia infections are common in several bird populations that have contact with humans -- aquatic birds that may visit reservoirs or beaches, pets such as parrots and lovebirds, and pests such as pigeons -- and it is speculated that zoonotic transfer may occur. Although most people can rapidly clear such an infection, immunocompromised people such as children, the elderly, and HIV-infected individuals are at risk for serious complications. Improving the sensitivity and/or specificity of microsporidia diagnosis could thus be useful in environmental testing and subsequent health care recommendations. Your class-wide study of animal/environmental bacteria populations has similar implications for managing disease risk.

We thank the Runstadler lab for access to bird samples (pre-screened for flu and everything!), and especially Wendy Puryear for helpful technical discussions as this module was developed. We also thank Professor Karen Snowden at Texas A & M University for access to microsporidia spores and for invaluable advice about imaging methods for identifying microsporidia.

Module 1 Conceptual Overview. Experimental goals are shown in yellow, related concepts in blue, and related application areas in green. Stars span both experiments, while triangles are associated with a single experiment.
Module 1 Conceptual Overview. Experimental goals are shown in yellow, related concepts in blue, and related application areas in green. Stars span both experiments, while triangles are associated with a single experiment.


Module 1 Day 1: Context-setting and primer design
Module 1 Day 2: DNA extraction
Module 1 Day 3: PCR and paper discussion

Note: 1 week between day 3 and day 4.

Module 1 Day 4: DNA cloning
Module 1 Day 5: DNA sequencing and primer analysis
Module 1 Day 6: Journal club I
Module 1 Day 7: Phylogenetic analysis
Module 1 Day 8: Journal club II

Laboratory Report
Primer design summary

TA notes, mod 1
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